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Poppr: An R package for population genetics

Poppr is an R package useful in analysis of population genetic data. Poppr introduces core functions for analysis of populations with mixed modes of reproduction typically observed for microbial populations including a blend of asexual and sexual reproduction. Poppr allows for convenient hierarchical analysis of populations with multiple subpopulation levels, clone censoring, distance analysis (including Bruvo's distance) including dendrograms with bootstrap support, linkage disequilibrium and more. Please check back as we continue writing this primer. Currently, poppr is available on CRAN with development versions on github. A PDF manual is also available for download providing documentation on how to use poppr. Please feel free to contact the authors for feedback and bugs. We intend to continue to improve and maintain poppr.